Resonant cavity biosensor

ABSTRACT

An assay system having a channel bounded by first and second reflective surfaces adapted to accommodate a fluid material therebetween and defining a plurality of regions in an array between those surfaces with each region defining a resonant cavity and adapted to receive a capturing material on a surface thereof whereby a source of radiation illuminates each region to provide a standing wave of radiation of within the cavity indicative of binding of said capturing agent to material under investigation, a binding thereof being detected in response to radiation from each cavity indicative of a change in the standing wave pattern.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to commonly assigned ProvisionalApplication Ser. No. 60/455,970 filed Mar. 19, 2003 and InternationalPatent Application Number PCT US2004/008558 filed on Mar. 19, 2004.International Application No. PCT/US00/12287, filed 5 May 2000 isincorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

N/A

BACKGROUND OF THE INVENTION

In bio-research, ecological testing, medical testing, drug testing andbio-weapon and hazards detections there is a need for rapid,simultaneous and real time detection of various agents. Typically theagents are provided in a fluid to a test structure, generally an arrayof some form in which capturing materials of diverse types capable ofbinding to one or more of the materials undergoing test and provided inthe fluid medium. The binding is a result of an affinity that moleculesor bio-molecules have for each other and includes the affinities of DNA,RNA, proteins, small molecules and other molecules. DNA arrays andprotein arrays, commonly called DNA or protein chips, are twotechnologies used for bio-molecule affinity sensing in such fields asgenomics and proteomics.

The array of capturing materials is created in a known pattern such thatby correlation of the binding response of the capturing material to thefluid born molecules under test, it is possible by detecting the levelof binding at each array element to determine what materials under testare present. In one case of DNA or RNA testing, various sequences of theDNA or RNA molecule are affixed to corresponding locations in the array.DNA or RNA in the fluid being tested will tend to bind where thesequences therein strongly match the sequences attached to the variousarray sites.

Test methods known to date fail to provide high throughput, real timeoperations or to avoid difficult labeling processes, or to avoidcapturing material incompatibility with metal sensor surface, requiringcumbersome linking chemistry that may adversely affect bindingproperties.

Among the techniques previously used which fail to provide all of theserequirements in combination are fluorescent tagging. Fluorescent taggingprocedures suffer from a number of problems including the difficulty oftagging and the possibility of tagging altering the binding properties.Moreover tagging procedures are difficult to monitor continuously inreal time. Among other techniques surface plasmon resonance is popular.This technique, however, requires the affixation of molecules to a metalsurface, particularly gold, which has the above mentionedincompatibility problem. Other techniques include waveguide techniquesand acoustic detection techniques. Neither of these accommodates a highthroughput, requiring a large number of array elements.

Finally, another known technique, reflectometric interferencespectroscopy, suffers from the complication of using multiple fiberprobes, which greatly hinders its ability to become high throughput.

BRIEF SUMMARY OF THE INVENTION

The present invention provides an affinity detection system which hashigh throughput, is real time and avoids the complexities of metal,cumbersome equipment and other deficiencies of prior art techniques.

According to the teaching of the present invention, an array ofbiosensor or capturing material elements is formed between first andsecond surfaces of reflective mirrors. Typically, the mirrors are formedby multi-layer dielectric surfaces selected to be reflective at aparticular range of wavelengths, commonly in the IR frequency regions.Light, typically from a laser, is applied through the array and focusedonto a photo-detection system such as a CCD chip or photodetector arraywhere each element of the capturing array is focused onto one or morepixels of the image chip.

A fluid containing materials under test flows through the array betweenthe surfaces forming the mirror elements, the material having anaffinity for a capturing material in one or more array cells. Instead ofa fluid (gas or liquid with particles or fluid components under test) asolid of appropriate transparency may be tested. These materials will bebound to the capturing material of that cell having such an affinitychanging the resonant properties of the resonant cavity formed betweenthe mirror surfaces in that cell. The result will be a change in thelight received by the corresponding CCD pixels. That change can bedetected by processing electronics correlating the position of thechange, its nature and the known affinity of that particular resonantcavity cell.

In this fashion, a large number of bio-molecules or other molecules canbe tested for in real time. Array dimensions of hundreds of thousands ormillions of cells are possible and the processing electronics availabletoday can easily provide a real time indication of the nature ofmolecules present in a medium being tested.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

These and other features of the present invention are described in thefollowing detailed description taken in conjunction with the drawing ofwhich:

FIG. 1 is a diagram illustrating the components of a testing system ofthe present invention;

FIG. 2 illustrates an array of bio-probes according to the invention;

FIG. 3 illustrates an array of photo-detectors such as a photodetectorarray for use in the present invention or alternatively as a multi-celllight source according to an embodiment of the invention;

FIG. 4 illustrates the operation of a single cell in response toincident light according to the invention;

FIG. 5 illustrates a standing wave pattern typical of the presentinvention when exposed to illumination;

FIGS. 6A and 6B illustrate the variation in cell sensitivity as afunction of dielectric layers in opposing mirrors according to theinvention;

FIGS. 7A and 7B illustrate the change in resonant wavelength with thecavity narrowing from binding of molecules at different cavitydimensions and mirror compositions;

FIGS. 8A, 8B and 8C illustrate the variation of cavity mirrortransmittance as a function of wavelength with cavity mirror dielectriclayer complexity;

FIGS. 9A and 9B illustrate resonance under differing conditions usefulin understanding the invention;

FIGS. 10A through 10E illustrate and example of the invention in actualtest use;

FIG. 11 illustrates an embodiment with an integral photodetector; and

FIG. 12 illustrates a system for testing multiple arrays on a continuousbasis.

DETAILED DESCRIPTION OF THE INVENTION

FIG. 1 illustrates an optical control system according to the inventionin which a wavelength tunable laser 1, which may be an Aristu MNG638Aprovides output radiation typically in the vicinity of 1560 nanometers(15,600 Angstroms) to a single mode optical fiber 2. Radiation in thefiber 2 is applied to an optical attenuator 3, which may be an Agilent85156A. The attenuator provides dynamic adjustment consistency topromote the operation of the system as a whole as described below. Inorder to provide beam cleaning which insures a Gaussian distribution tothe spatial intensity profile of the beam, the output of the attenuator3 is applied through a long coil of single mode fiber 4, typically 5 Km.The thus cleaned light is applied through a fiber collimator 5 whichuses an antireflective coated objective at 1550 nanometers. Thecollimator produces a 1 mm beam, the diameter being measured betweenhalf maximum intensity points.

The collimated beam 6 is applied to an optical system comprising a lens7 which is in the exemplary example a 15 mm focal length antireflectivecoated lens. The converging beam from the lens 7 is applied through a 50micron aperture 8 placed at the focal point 9 of the beam from the lens7. The function of the 50 micron aperture is to provide further beamcleaning. The thus clean beam is applied to a further antireflectivecoated lens 10, typically of a 125 mm focal length. The lens 10 producesa collimated beam 11, in this example of 10 mm width between halfmaximum intensity points. The beam 11 is reflected at right angles by a45° mirror 12 into the array of cells. This optical system may be amicroscope system.

The detection system comprises a cavity 16 formed between first andsecond reflecting surfaces 14 and 15 separated by a space within which astanding wave is generated by the radiation in beam 11. That radiationis applied through a lower support 17, aperture 18 into a lower or firststage 19 through a further aperture 20.

The second reflective surface 15 is supported by a second stage 21supported by a second support 22. Adjusters 23 and 24 allow adjustmentof the first stage 19 with respect to the first support 17 while amicrometer 25 provides a similar function for the second stage 21 withrespect to the support 22.

The light in beam 11 creates a standing wave pattern in the cavity 16,particularly one dependent upon the characteristics of a capturingmaterial applied to each cell in an array on the mirror 14, all asdescribed more completely herein below. Light of an intensity dependantupon the degree of resonance within each cell travels in a beam 30through a focusing lens 31 to a camera 32, typically by reflection froma 45° mirror 33. The camera 32, which may be a Sensors UnlimitedSU128-1.7R camera having a InGaAs sensor with pixels in a 128×128 array,receives that light. Typically, each cell will be imaged onto one ormore pixels in the array of camera 32. The image from camera 32 is readinto a computer 34 to an image acquisition card 35, which may typicallybe a National Instrument NI-PCI1422. The computer 34 has a controllercard 36, typically a GPIB card, which applies control signals to thetunable laser 1. The card 36 also operates through a piezoelectriccontroller 37 to control piezoelectric actuators on the adjusters 23 and24, typically placed at their tips where they join the first stage 19.The computer 34 may have an input/output interface 38 for communicationwith users, networks, printers display and other typical computeraccessories.

The computer maintains a feedback loop through the piezoelectriccontroller 37 on the adjusters 23 and 24 via the camera 32 to sensefringe patterns in the optical image received and processed by thecamera 32 which are an indication of an out of parallel conditionbetween the stages 19 and 21, using known minimization techniques, thepiezoelectric drives are operated to minimize those fringing elementsthereby obtaining a parallel condition of the stages 19 and 21. Thepiezo elements are also operable by the computer to vary the spacingbetween reflectors as an alternative or complementary to wavelengthscanning of the laser radiation.

A heating element 42 operates with a heat control unit 43 which may ormay not have a connection to computer 34 in order to maintain or controlthe temperature between the stages 19 and 21 and in particular withinthe cavity region 16 where standing wave patterns are created by theincident illumination. This heat control accomplishes the function ofavoiding dynamic changes on the mirrors during testing.

The computer 34 is programmed to process the image data from each pixelreceived by the camera 32 in order to determine the thickness betweenthe reflectors 14 and 15 in each cell, representative of the binding ofmaterial flowed through the intermirror, cavity region 16 for biologicor chemical assay purposes. This process includes the steps of:

1. Low pass filtering the intensity wavelength response curves for eachpixel with respect to wavelength;

2. Cross-correlating the local overlapping groups of pixels to findrelative shifts in the intensity wavelength profile;

3. Solving an over-determined problem which involves integrating theshifts to find a consistent picture of capturing material surfacethickness.

In order to develop an intensity wavelength response, the computer 34will typically cause the tunable laser 1 to scan through a set ofwavelengths.

In the operation of the feedback control of mirror alignment, if thereis an angle between the two mirrors 14 and 15, such that the distancebetween them changes by more than a half wavelength, the cavity 16 willbe resonant in some places and non-resonant at others. Everywhere theresonance condition is satisfied, the camera 32 and computer 34 will seebright spots on the camera monitoring transmission. For a perfectly flatmirror at an angle, this amounts to horizontal lines indicating equalcavity spacing where resonance is satisfied. As one of the angles istuned, the lines grow closer together or farther apart. Closer together,indicates that the angle perpendicular to the lines is growing steeper.As one of the adjustment knobs is tuned far to one end, the lines willgrow increasing close together and increasing perpendicular to thatangle. If the same knob is turned the other direction, the lines growcloser and less perpendicular to that angle. As the knob is keptturning, the lines will go through an optimal position after which theywill again start to grow closer together and more perpendicular to thedirection of angle change. By adjusting very carefully, one can tune tothat optimal position where the lines would start contracting again ifthere was movement in either direction of the tuning knob, and where thelines are actually parallel to the direction of the angle adjustment.This means that in this direction, the surface is completely flat. Thesame is repeated for the other direction. Once the other direction isdone, the first one has probably moved a bit due to vibration fromhandling of the system, so an iterative approach may be needed to someextent. Wavelength changes move the lines but not their orientation, andthe spacing between lines only changes slightly due to wavelength andcan be taken into account by simply realizing that it was due towavelength not angle change. Most often, we can not get to the pointthat the surface is completely lit due to surface curvature. A circle iseventually seen instead of the whole screen going bright, because thesurface is curved and satisfying the resonant condition at only placeson the circle, no matter how parallel the mirrors 14 and 15 are. Whenthis circle is visible, the mirrors 14 and 15 are reasonably paralleland tuning can stop.

The peizo/computer control can take over this function and it allowsmuch finer adjustment, making it easier to tune. The peizos do notdisturb the system like the hand of a human operator on the adjusters 23and 24 does. It is then possible to control the system to keep themirrors 14 and 15 parallel throughout the operation of the biosensor.

FIG. 2 illustrates an array of cells 80, typically those which may beapplied to the surface of mirror 14 in bio or protein chips of knowndesign. Hundreds of thousands or even millions of cells 80 can beprovided in the mirror 14 within the cavity region 16. These cells 80,as noted above, are typically imaged into one or more pixels 82 of aphotodetector array 84 in FIG. 3 within the multi-channel detector 30.Alternatively, the pattern illustrated by FIG. 3 can represent thepattern of light emitters such as from laser diodes. The memoryassociated with processor 34 will correlate one or more of the pixels 82of the photodetector array 84 to corresponding cells 80 and theparticular molecular affinity of the material bonded to the mirror 14,typically to several angstroms in depth.

FIG. 4 illustrates diagrammatically the operation of a single cell 80 ofthe detection system of the present invention. The cell has a thin layerof a capturing material 90 affixed to it at each cell 80. The opticalthickness of this material may be 5 angstroms and when binding occurswith molecules for which the capturing material there has an affinitythe optical thickness may increase by as much as 10 angstroms.

Light from the laser 1 provides wavefronts 100 which pass into thecavity region 16 through mirror 12 and are reflective within the cavity16 by the reflectance of the mirrors 14 and 15 to the wavelength and theincident radiation 100. As molecules in the flow through cavity 16 bindto the capturing material 90, the wavelength response will shift from anoriginal array 102 in FIG. 4A to a shifted wavelength response 104 inFIG. 4B.

FIG. 5 illustrates in greater detail the mirrors 14 and 15 as consistingof a plurality of alternating silicon and silicon dioxide dielectriclayers 106 and 108, respectively. As illustrated in FIG. 5, the surfaceof the first mirror 14 will typically be terminated with an extrasilicon dioxide layer 108 causing a standing wave pattern 110 within thecavity region 16 illustrated in FIG. 5 to have a peak 112 at the outerwall of the layer 108. This maximizes the effectiveness and sensitivityof the detection system of the present invention.

This effect is more clearly illustrated in FIGS. 6A and 6B andaccompanying, corresponding FIGS. 7A and 7B. FIG. 6A illustratessubstantially the standing wave pattern and dielectric layer scheme ofFIG. 5. FIG. 7A illustrates the wavelength shift corresponding to a 5nanometer buildup of material at the corresponding cell.

FIG. 6B illustrates the case where the standing wave pattern is aminimum at the front of the mirror 14 and the corresponding relativelyinsignificant change in resonant wavelength for a 5 nanometer buildupbeing illustrated in FIG. 7B.

In FIG. 7A:

Cavity is 50 micron cavity filled with a buffer solution;

Left curve is for 5 Angstroms of biomaterial;

Right curve is for 10 Angstroms of biomaterial;

270 nm extra SiO2 layer is present to maximize sensitivity;

AR coating is present on mirror backsides;

X-axis is wavelength in nm;

Y-axis is transmission;

Curves shifted 0.004 nm.

In FIG. 7B:

Cavity is 50 micron cavity filled with a buffer solution;

Left curve is for 5 Angstroms of biomaterial;

Right curve is for 10 Angstroms of biomaterial;

No extra SiO2 layer is present to maximize sensitivity;

AR coating is present on mirror backsides;

X-axis is wavelength in nm;

Y-axis is transmission;

Curves nearly indistinguishable; Curves shifted 0 nm.

FIGS. 8A and 8C illustrate the sensitivity increase as the number ofdielectric layers within the mirrors 15 and 14 increases essentiallyforming a Bragg reflector. FIGS. 8A-8B curves represent computersimulations corresponding, from left to right, to 2 sets of alternatinghigh and low index layers, 3 sets, and 4 sets in the far right. Thecalculations use a solution index of refraction of 1.33 and the materialis calculated with an index of refraction of 1.45. The capturingmaterial layer is 0.05 nanometers while the target/capture layerthickness is 0.1 nanometers.

The embodiments of the invention may vary. In particular, the wavelengthof the applied radiation may be other than within the infrared or IRbands, the radiation applied to the mirrors 15 and 14 may be other thanorthogonal and the mirrors 15 and 14 may not necessarily be parallel.The processor and photodetector array, while typically measuring lightamplitude as an indication of affinity binding, may detect phase,polarization or actual frequency shifts. The tuning of the laser 36 maybe continuous or in discrete steps. A VCSEL array may alternatively beused as a source of radiation as well as laser diodes.

Simulation

FIGS. 9A-9B show a simulation of wavelength shifts.

In FIG. 9A:

Cavity is 10 micron cavity filled with a buffer solution;

Left curve is for 5 Angstroms of biomaterial;

Right curve is for 10 Angstroms of biomaterial;

270 nm extra SiO2 layer is present to maximize sensitivity;

AR coating is present on mirror backsides;

X-axis is wavelength in nm;

Y-axis is transmission;

Curves shifted 0.012 nm.

In FIG. 9B:

Cavity is 100 micron cavity filled with a buffer solution;

Left curve is for 5 Angstroms of biomaterial;

Right curve is for 10 Angstroms of biomaterial;

270 nm extra SiO2 layer is present to maximize sensitivity;

AR coating is present on mirror backsides;

X-axis is wavelength in nm;

Y-axis is transmission;

Curves shifted 0.001 nm.

EXAMPLE

Fabrication of test sample: A test pattern has been fabricated in SiO2to test that the system is working (FIG. 10A). 270 nm of SiO2 wasdeposited on the top surface of the first reflector. This SiO2 layerserves to place the sensing surface at a position in the cavity wherethe field strength is high (approximately 1 quarter wavelength out fromthe reflector surface at the wavelengths we are scanning at). The SiO2surface was then masked and lightly etched to leave 4 square features.The 4 squares are 50 μm×50 μm and 30 μm apart. The pattern is repeatedevery 500 μm. The sample was masked at the boxes and wet etchedeverywhere else using HF to remove approximately 15 nm of material. 4boxes 50 μm×50 μm×15 nm should remain on top of 255 nm SiO2, on top ofthe reflector.

Running experiment: Micrometers were used to position the reflectorsclose to each other to form the cavity. A z-stage was used to translateone of the reflectors to approximately 100 μm away from the other, toform a 100 μm air cavity. Fringes could be seen on the video output fromthe camera, indicating that the reflectors were not parallel. An anglestage holding the other reflector was then carefully adjusted until thefringes could no longer be seen. Wavelength was scanned from 1545 nm to1560 nm in 0.01 nm steps. An image of the cavity was captured at eachstep with approximately 6× magnification (FIGS. 10B and 10C out and inresonance).

Processing data: The resulting wavelength response curve for each pixelwas then low pass filtered with a 5 samples/nm cutoff. The data werethen broken down into groups of 9 waveforms taken from 3×3 sets ofneighboring pixels. The groupings were made so that they overlap by 1row or column of pixels with neighboring groups of 3×3. Within each 3×3group, the 9 wavelength response curves were cross correlated to eachother. The peak of the cross-correlations indicates the shift betweenthose two waveforms. Nine (9) waveforms cross correlating with eachother produces 81 correlations, including 9 auto correlations, whichleads to 72 shifts describing the relative position of each pixel withrespect to the other 8 pixels. This information is heavily redundant. Alinear systems over determined problem was setup and solved to find 8shifts for 8 of the pixels relative to the top left most pixel which wasgiven the shift of zero. This was done for all of the overlapping groupsof 3×3 pixels. The top left most group of 3×3 pixels was designated tohave a zero overall offset. The offset of the other 3×3 groupingsrelative to this first 3×3 group was then determined. The offset foreach of the 3×3 groupings was found from solving a linear systems overdetermined problem as well, where the equations are derived from thefact that the 3×3 groupings overlap by columns and rows that must beconsistently the same height. The solution of this problem provided anoverall offset for each of the 3×3 groups. The final result is a meshwhere the height of each pixel indicates the shift between itswavelength response and that of the upper left most pixel on the camera.There are two key advantages to this technique. First, only localwaveforms are ever correlated directly. This is important because thewavelength response drifts in overall shape across the sensor surfacedue to inhomogeneous illumination and curvature of the mirror structure.Comparing only local pixels, we are more assured that the resonantwaveform has the same shape and its only the shift we are measuring.Secondly, by comparing each pixel to 8 of its neighbors, redundancy isgained which is used to improve the accuracy of the observed shift overa correlation done between just two pixels.

Interpreting the results: The four boxes of FIG. 10E in the mesh reflectthe results. The boxes appear to be approximately 10 steps high. Thesteps indicated on the z-axis correspond to the 0.01 nm steps inwavelength that were taken.

The best sensitivity we could attain by including the extra SiO2 layerwould be a 2/m shift in wavelength for a corresponding shift in surfaceheight where m is the mode number given by m=2*d/lambda, lambda beingthe wavelength and d being the cavity size. For a 100 μm cavity andwavelengths in the neighborhood of 1.55 μm, the sensitivity would be0.0155 nm shift in wavelength response for a 1 nm shift in sensorsurface height. Alternatively stated, every 1 nm shift in wavelengthindicates a 65 nm (1/0.0155) shift in sensor surface height. Again, thisassumes a quarter-wavelength of SiO2 on the reflector surface. As thisSiO2 layer would differ towards a half wave thickness, or zerothickness, the sensitivity would fall to 0.

With this in mind, we see that the 10 steps for the features in the meshsurface plot indicates a 0.1 nm shift in wavelength, which indicates a6.5 nm step in the sensor surface. The target height of the features was15 nm.

In FIG. 10A:

Model of SiO2 pattern created by photolithography and wet HF etch.

Surface sits on top of quarter wavelength layer of SiO2 (270 nm) formaximized sensitivity.

In FIGS. 10B and C:

View from camera at one fixed wavelength (lambda=1559.70 nm).Approximately 6× magnification so that each pixel representsapproximately 10 microns square.

At most wavelengths the image is completely dark, and at a few, itsnearly all bright. Here, at lambda=1559.70 nm, most of the surface is onits way to resonance (bright), but the 4 apparent squares in the upperright are lagging because of their shifted response.

In FIG. 10D:

Bottom axis shows wavelength in nanometers. Vertical axis indicatesrelative intensity as measured by camera pixel. Previous image was takenat 1559.70 nm where we can see that the intensity was on the rise atthis pixel, but not maximum. On the transition, the contrast ismaximized and one is able to discern the 4 square features.

Here is the final mesh of shift vs. pixel position. The horizontal axesindicate pixel (this is a 40×40 section taken from the 128×128 array forclarity). The vertical axis indicates by how many steps the response wasshifted relative to the bottom most corner pixel which was designated ashaving a 0 shift. The data was taken in steps of lambda=0.01 nm, so thatthe features, which appear to be 10 steps high, corresponds to a 0.1 nmshift in wavelength for their response. For this 100 μm cavity, everynanometer shift in resonant response indicates a 65 nm shift, so thatthese features would appear to be 6.5 nm in height.

Finally, the processing while still substantially real time may involveother or alternative mathematical techniques such as averaging,differentiating, integrating, curve fitting (in lieu of correlating), orcorrelating or otherwise comparing various frames or pixels of themulti-channel detector.

FIG. 11 illustrates an embodiment where the photodetector is provided onthe exit mirror as an array 140 on a substrate 142, which may besilicon. Here as throughout the optical path an anti-reflective coating144 is provided between them. Dialectric layers 146 are at the bottom ofthe substrate to provide the reflectivity described above. The bottomreflector structure 148 as above comprises a substrate 150, bottomcoating 152 anti-reflective to the incident collimated beam 154. Thesubstrate 150 has dielectric layers 156 and a silicon dioxide layer 158on which the array of capturing material 160 is placed.

FIG. 12 is an embodiment where plural testing units such as the bottomreflector structure 148 are passed under the upper reflector structure162 of the type described above on a conveyor system 160. The light fromthe upper structure 162 after passing through the cavity 164 testmaterial and capturing material 166 is received at a detection system168 which may be as described above.

The invention described herein is to be limited only in accordance withthe following claims:

1. An assay system comprising: first and second reflective surfaces thatare structured and arranged to provide a channel therebetween, toaccommodate a fluid having material to be tested, at least one of thefirst and second reflective surfaces having capturing material disposedin an array pattern, the array pattern having a plurality of resonantcavity regions between said first and said second reflective surfaces; asource of radiation to illuminate each cavity region at a wavelengthadapted to provide a standing wave of radiation within each said cavityregion; a radiation detector that is structured and arranged to detect achange in a standing wave pattern, which is indicative of binding of thecapturing material with the material to be tested in the fluid withineach said cavity region; and means for dynamically varying spacing ofsaid first and second surfaces.
 2. An assay system comprising: first andsecond reflective surfaces that are structured and arranged to provide achannel therebetween, to accommodate a fluid having material to betested; a plurality of regions in a pattern of an array between saidfirst and surfaces, each region defining a cavity and having a capturingmaterial on one of the first and second surfaces therein; a source ofwavelength scanned radiation to illuminate each region at a wavelengthadapted to provide a transmission of that radiation within each saidcavity representative of material from said fluid bound to saidcapturing material; a detector for the transmitted radiation in eachsaid cavity and operative to indicate a level of binding by saidcapturing material to said material to be tested in said fluid withineach said cavity; and means for dynamically varying spacing of saidfirst and second surfaces.
 3. The assay system of claim 1 wherein saidfirst and second reflective surfaces include one or more dielectriclayers forming said corresponding reflective surface at a wavelengthcorresponding to said standing wave pattern.
 4. The assay system ofclaim 1 wherein said capturing material as applied to each cavity formsa DNA or protein chip where individual capturing materials in eachcavity are DNA or protein selective.
 5. The assay system of claim 1wherein said radiation source is an IR source.
 6. The assay system ofclaim 1 wherein said radiation source is a laser source.
 7. The assaysystem of claim 1 wherein said radiation source is a tunable lasersource.
 8. The assay system of claim 6 further including means forscanning said tunable laser through a range of wavelengths including awavelength corresponding to said standing wave pattern in each cavity.9. The assay system of claim 1 further including a beam expander in apath of radiation between said radiation source and said channel. 10.The assay system of claim 1 further including a beam condenser in a pathof radiation between said channel and said detector.
 11. The assaysystem of claim 1 wherein said detector includes a multi elementdetector wherein each element receives radiation from a correspondingcavity.
 12. The assay system of claim 1 wherein said detector is a CCDdetector.
 13. The assay system of claim 1 wherein said first and saidsecond reflective surfaces are parallel and radiation from said sourceis applied othogonally to said first and second reflective surfaces. 14.The assay system of claim 1 wherein said radiation is applied obliquelyto at least one of said first and second surfaces.
 15. The assay systemof claim 1 wherein said detector detects one or more of radiationamplitude, phase, polarization and wavelength.
 16. The assay system ofclaim 1 wherein said source of radiation includes means for causing saidradiation to emit at discrete different wavelengths.
 17. The assaysystem of claim 1 further including means for controlling a temperatureof the fluid within said channel.
 18. The assay system of claim 1wherein said detection system includes a photodetector array integralwith a support for one of said reflective surfaces which is notsupporting a capturing material.
 19. The assay system of claim 1 whereinsaid at least one reflective surface having said capturing materialthereon has an added dielectric layer to provide a peak in a standingwave pattern in said cavity at said capturing material.
 20. The assaysystem of claim 1 further including means for varying the spacing ofsaid reflective surfaces to vary the cavity resonance condition.
 21. Amethod for assaying a material under test, the method comprising:providing a channel bounded by first and second reflective surfacesadapted to accommodate at least one of the material under test and afluid containing the material under test therebetween; providing aplurality of regions to one of said first and second reflective surfacesin an array of capturing material elements to form a correspondingplurality of resonant cavities; applying a capturing material to thecapturing material elements in the array on one of the first and secondsurfaces; dynamically varying a spacing between said first and secondreflective surfaces, to maintain said reflective surfaces in parallelthroughout the method; passing the material under test or flowing thefluid containing the material through the channel; applying radiation asthe fluid flows past or the material under test passes each region toilluminate each region at a wavelength adapted to provide a standingwave of radiation within each said resonant cavity; and measuring theradiation in each said resonant cavity; and detecting a change inresonant properties of the standing wave pattern, which is indicative ofbinding of the material under test to the capturing material at eachsaid resonant cavity.
 22. A method for assaying a material under test,the method comprising: providing a channel bounded by first and secondreflective surfaces adapted to accommodate at least one of the materialunder test and a fluid containing the material under test therebetween;providing a plurality of regions to one of said first and secondreflective surfaces in an array of capturing material elements betweensaid first and second reflective surfaces; applying a capturing materialto the capturing material elements; dynamically varying a spacingbetween said first and second reflective surfaces, to maintain saidreflective surfaces in parallel throughout the method; passing thematerial under test or flowing the fluid containing the material throughthe channel; applying radiation as the fluid flows past or the materialunder test passes each region to illuminate each region at a wavelengthadapted to provide a standing wave of radiation within each saidresonant cavity; and measuring the radiation in each said resonantcavity; and detecting a change in resonant properties of the standingwave pattern, which is indicative of binding of the material under testto the capturing material at each said resonant cavity.
 23. The assaymethod of claim 21 wherein said first and second reflective surfacesinclude one or more dielectric layers forming said reflective surface ata wavelength corresponding to said standing wave pattern.
 24. The assaymethod of claim 23 further comprising: applying said capturing materialto each cavity in a DNA chip or protein chip format such that individualcapturing materials in each resonant cavity are DNA or proteinselective.
 25. The assay method of claim 23 wherein said radiation isIR.
 26. The assay method of claim 23 wherein said radiation is laserradiation.
 27. The assay method of claim 23 including the step of tuningsaid radiation.
 28. The assay method of claim 27 further including thestep of scanning said radiation through a range of wavelengths includinga wavelength corresponding to said standing wave pattern in each cavity.29. The assay method of claim 23 further including the step of expandingsaid radiation in a beam along a path of radiation between saidradiation source and said channel.
 30. The assay method of claim 23further including the step of condensing a beam of radiation along apath of radiation between said channel and said detector.
 31. The assaymethod of claim 23 wherein said detecting step includes detecting ineach of a plurality of detection elements wherein each element receivesradiation from a corresponding cavity.
 32. The assay method of claim 23wherein said first and second surfaces are parallel and radiation fromsaid source is applied othogonally to said first and second surfaces.33. The assay method of claim 23 wherein said radiation is appliedobliquely to at least one of said first and second surfaces.
 34. Theassay method of claim 23 wherein said detection step detects one or moreof radiation amplitude, phase, polarization and wavelength.
 35. Theassay method of claim 23 wherein said radiation is emitted at discrete,different wavelengths.
 36. The assay method of claim 23 furtherincluding the step of controlling a temperature of the fluid within saidchannel.
 37. The assaying method of claim 23 wherein said detecting stepincludes detecting at a photodetector array integral with a support forone of said reflective surfaces which is not supporting a capturingmaterial.
 38. The assaying method of claim 23 wherein said reflectivesurface is provided having said capturing material thereon has an addeddielectric layer to provide a peak in a standing wave pattern in saidcavity at said capturing material.
 39. The assay system of claim 23further including varying the spacing of said reflective surfaces tovary the cavity resonance conditions.
 40. An assay system comprising:first and second reflective surfaces that are structured and arranged todefine a space therebetween, the space being adapted to accommodatetherebetween a material to be tested; a plurality of regions in apattern of an array between said first and said second reflectivesurfaces, each region defining a resonant cavity between the first andsecond reflective surfaces therein and having capturing material on atleast one reflective surface; a source of radiation to illuminate eachregion at a wavelength adapted to provide a standing wave of radiationwithin each said resonant cavity; a detector for the radiation in eachsaid resonant cavity and operative to indicate a change in the standingwave pattern, which is reflective of the binding of said material to betested to the capturing material within each said resonant cavity; andmeans for dynamically varying spacing of said first and secondreflective surfaces.
 41. An assay system comprising: first and secondreflective surfaces that are structured and arranged to define a channeltherebetween, the channel being adapted to accommodate a material to betested; a plurality of regions in a pattern of an array between saidfirst and said second reflective surfaces, each region defining aresonant cavity between the first and second reflective surfaces thereinand having capturing material on at least one reflective surface; asource of wavelength scanned radiation to illuminate each region at awavelength adapted to provide a transmission of that radiation withineach said resonant cavity representative of said material to be testedbound to the capturing material in each resonant cavity; a detector forthe radiation in each said resonant cavity and operative to indicate alevel of binding of the capturing material to the material to be testedwithin each said resonant cavity; and means for dynamically varyingspacing of said first and second reflective surfaces.